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Mar 17

Assessment of Data Consistency through Cascades of Independently Recurrent Inference Machines for fast and robust accelerated MRI reconstruction

Machine Learning methods can learn how to reconstruct Magnetic Resonance Images and thereby accelerate acquisition, which is of paramount importance to the clinical workflow. Physics-informed networks incorporate the forward model of accelerated MRI reconstruction in the learning process. With increasing network complexity, robustness is not ensured when reconstructing data unseen during training. We aim to embed data consistency (DC) in deep networks while balancing the degree of network complexity. While doing so, we will assess whether either explicit or implicit enforcement of DC in varying network architectures is preferred to optimize performance. We propose a scheme called Cascades of Independently Recurrent Inference Machines (CIRIM) to assess DC through unrolled optimization. Herein we assess DC both implicitly by gradient descent and explicitly by a designed term. Extensive comparison of the CIRIM to CS as well as to other methods is performed: the E2EVN, CascadeNet, KIKINet, LPDNet, RIM, IRIM, and UNet. Models were trained and evaluated on T1-weighted and FLAIR contrast brain data, and T2-weighted knee data. Both 1D and 2D undersampling patterns were evaluated. Robustness was tested by reconstructing 7.5x prospectively undersampled 3D FLAIR MRI data of Multiple Sclerosis (MS) patients with white matter lesions. The CIRIM performed best when implicitly enforcing DC, while the E2EVN required an explicit DC formulation. In reconstructing MS patient data, prospectively acquired with a sampling pattern unseen during model training, the CIRIM maintained lesion contrast while efficiently denoising the images. The CIRIM showed highly promising generalization capabilities maintaining a very fair trade-off between reconstructed image quality and fast reconstruction times, which is crucial in the clinical workflow.

R2D2: Reducing Redundancy and Duplication in Data Lakes

Enterprise data lakes often suffer from substantial amounts of duplicate and redundant data, with data volumes ranging from terabytes to petabytes. This leads to both increased storage costs and unnecessarily high maintenance costs for these datasets. In this work, we focus on identifying and reducing redundancy in enterprise data lakes by addressing the problem of 'dataset containment'. To the best of our knowledge, this is one of the first works that addresses table-level containment at a large scale. We propose R2D2: a three-step hierarchical pipeline that efficiently identifies almost all instances of containment by progressively reducing the search space in the data lake. It first builds (i) a schema containment graph, followed by (ii) statistical min-max pruning, and finally, (iii) content level pruning. We further propose minimizing the total storage and access costs by optimally identifying redundant datasets that can be deleted (and reconstructed on demand) while respecting latency constraints. We implement our system on Azure Databricks clusters using Apache Spark for enterprise data stored in ADLS Gen2, and on AWS clusters for open-source data. In contrast to existing modified baselines that are inaccurate or take several days to run, our pipeline can process an enterprise customer data lake at the TB scale in approximately 5 hours with high accuracy. We present theoretical results as well as extensive empirical validation on both enterprise (scale of TBs) and open-source datasets (scale of MBs - GBs), which showcase the effectiveness of our pipeline.

Valentine: Evaluating Matching Techniques for Dataset Discovery

Data scientists today search large data lakes to discover and integrate datasets. In order to bring together disparate data sources, dataset discovery methods rely on some form of schema matching: the process of establishing correspondences between datasets. Traditionally, schema matching has been used to find matching pairs of columns between a source and a target schema. However, the use of schema matching in dataset discovery methods differs from its original use. Nowadays schema matching serves as a building block for indicating and ranking inter-dataset relationships. Surprisingly, although a discovery method's success relies highly on the quality of the underlying matching algorithms, the latest discovery methods employ existing schema matching algorithms in an ad-hoc fashion due to the lack of openly-available datasets with ground truth, reference method implementations, and evaluation metrics. In this paper, we aim to rectify the problem of evaluating the effectiveness and efficiency of schema matching methods for the specific needs of dataset discovery. To this end, we propose Valentine, an extensible open-source experiment suite to execute and organize large-scale automated matching experiments on tabular data. Valentine includes implementations of seminal schema matching methods that we either implemented from scratch (due to absence of open source code) or imported from open repositories. The contributions of Valentine are: i) the definition of four schema matching scenarios as encountered in dataset discovery methods, ii) a principled dataset fabrication process tailored to the scope of dataset discovery methods and iii) the most comprehensive evaluation of schema matching techniques to date, offering insight on the strengths and weaknesses of existing techniques, that can serve as a guide for employing schema matching in future dataset discovery methods.

Aligning benchmark datasets for table structure recognition

Benchmark datasets for table structure recognition (TSR) must be carefully processed to ensure they are annotated consistently. However, even if a dataset's annotations are self-consistent, there may be significant inconsistency across datasets, which can harm the performance of models trained and evaluated on them. In this work, we show that aligning these benchmarksx2014removing both errors and inconsistency between themx2014improves model performance significantly. We demonstrate this through a data-centric approach where we adopt a single model architecture, the Table Transformer (TATR), that we hold fixed throughout. Baseline exact match accuracy for TATR evaluated on the ICDAR-2013 benchmark is 65% when trained on PubTables-1M, 42% when trained on FinTabNet, and 69% combined. After reducing annotation mistakes and inter-dataset inconsistency, performance of TATR evaluated on ICDAR-2013 increases substantially to 75% when trained on PubTables-1M, 65% when trained on FinTabNet, and 81% combined. We show through ablations over the modification steps that canonicalization of the table annotations has a significantly positive effect on performance, while other choices balance necessary trade-offs that arise when deciding a benchmark dataset's final composition. Overall we believe our work has significant implications for benchmark design for TSR and potentially other tasks as well. All dataset processing and training code will be released.

Improved Techniques for Training Consistency Models

Consistency models are a nascent family of generative models that can sample high quality data in one step without the need for adversarial training. Current consistency models achieve optimal sample quality by distilling from pre-trained diffusion models and employing learned metrics such as LPIPS. However, distillation limits the quality of consistency models to that of the pre-trained diffusion model, and LPIPS causes undesirable bias in evaluation. To tackle these challenges, we present improved techniques for consistency training, where consistency models learn directly from data without distillation. We delve into the theory behind consistency training and identify a previously overlooked flaw, which we address by eliminating Exponential Moving Average from the teacher consistency model. To replace learned metrics like LPIPS, we adopt Pseudo-Huber losses from robust statistics. Additionally, we introduce a lognormal noise schedule for the consistency training objective, and propose to double total discretization steps every set number of training iterations. Combined with better hyperparameter tuning, these modifications enable consistency models to achieve FID scores of 2.51 and 3.25 on CIFAR-10 and ImageNet 64times 64 respectively in a single sampling step. These scores mark a 3.5times and 4times improvement compared to prior consistency training approaches. Through two-step sampling, we further reduce FID scores to 2.24 and 2.77 on these two datasets, surpassing those obtained via distillation in both one-step and two-step settings, while narrowing the gap between consistency models and other state-of-the-art generative models.

Bidirectional Copy-Paste for Semi-Supervised Medical Image Segmentation

In semi-supervised medical image segmentation, there exist empirical mismatch problems between labeled and unlabeled data distribution. The knowledge learned from the labeled data may be largely discarded if treating labeled and unlabeled data separately or in an inconsistent manner. We propose a straightforward method for alleviating the problem - copy-pasting labeled and unlabeled data bidirectionally, in a simple Mean Teacher architecture. The method encourages unlabeled data to learn comprehensive common semantics from the labeled data in both inward and outward directions. More importantly, the consistent learning procedure for labeled and unlabeled data can largely reduce the empirical distribution gap. In detail, we copy-paste a random crop from a labeled image (foreground) onto an unlabeled image (background) and an unlabeled image (foreground) onto a labeled image (background), respectively. The two mixed images are fed into a Student network and supervised by the mixed supervisory signals of pseudo-labels and ground-truth. We reveal that the simple mechanism of copy-pasting bidirectionally between labeled and unlabeled data is good enough and the experiments show solid gains (e.g., over 21% Dice improvement on ACDC dataset with 5% labeled data) compared with other state-of-the-arts on various semi-supervised medical image segmentation datasets. Code is available at https://github.com/DeepMed-Lab-ECNU/BCP}.

ICON: Improving Inter-Report Consistency of Radiology Report Generation via Lesion-aware Mix-up Augmentation

Previous research on radiology report generation has made significant progress in terms of increasing the clinical accuracy of generated reports. In this paper, we emphasize another crucial quality that it should possess, i.e., inter-report consistency, which refers to the capability of generating consistent reports for semantically equivalent radiographs. This quality is even of greater significance than the overall report accuracy in terms of ensuring the system's credibility, as a system prone to providing conflicting results would severely erode users' trust. Regrettably, existing approaches struggle to maintain inter-report consistency, exhibiting biases towards common patterns and susceptibility to lesion variants. To address this issue, we propose ICON, which improves the inter-report consistency of radiology report generation. Aiming at enhancing the system's ability to capture the similarities in semantically equivalent lesions, our approach involves first extracting lesions from input images and examining their characteristics. Then, we introduce a lesion-aware mix-up augmentation technique to ensure that the representations of the semantically equivalent lesions align with the same attributes, by linearly interpolating them during the training phase. Extensive experiments on three publicly available chest X-ray datasets verify the effectiveness of our approach, both in terms of improving the consistency and accuracy of the generated reports.

Revisiting Table Detection Datasets for Visually Rich Documents

Table Detection has become a fundamental task for visually rich document understanding with the surging number of electronic documents. However, popular public datasets widely used in related studies have inherent limitations, including noisy and inconsistent samples, limited training samples, and limited data sources. These limitations make these datasets unreliable to evaluate the model performance and cannot reflect the actual capacity of models. Therefore, this study revisits some open datasets with high-quality annotations, identifies and cleans the noise, and aligns the annotation definitions of these datasets to merge a larger dataset, termed Open-Tables. Moreover, to enrich the data sources, we propose a new ICT-TD dataset using the PDF files of Information and Communication Technologies (ICT) commodities, a different domain containing unique samples that hardly appear in open datasets. To ensure the label quality of the dataset, we annotated the dataset manually following the guidance of a domain expert. The proposed dataset is challenging and can be a sample of actual cases in the business context. We built strong baselines using various state-of-the-art object detection models. Our experimental results show that the domain differences among existing open datasets are minor despite having different data sources. Our proposed Open-Tables and ICT-TD can provide a more reliable evaluation for models because of their high quality and consistent annotations. Besides, they are more suitable for cross-domain settings. Our experimental results show that in the cross-domain setting, benchmark models trained with cleaned Open-Tables dataset can achieve 0.6\%-2.6\% higher weighted average F1 than the corresponding ones trained with the noisy version of Open-Tables, demonstrating the reliability of the proposed datasets. The datasets are public available.

Curator: Efficient Indexing for Multi-Tenant Vector Databases

Vector databases have emerged as key enablers for bridging intelligent applications with unstructured data, providing generic search and management support for embedding vectors extracted from the raw unstructured data. As multiple data users can share the same database infrastructure, multi-tenancy support for vector databases is increasingly desirable. This hinges on an efficient filtered search operation, i.e., only querying the vectors accessible to a particular tenant. Multi-tenancy in vector databases is currently achieved by building either a single, shared index among all tenants, or a per-tenant index. The former optimizes for memory efficiency at the expense of search performance, while the latter does the opposite. Instead, this paper presents Curator, an in-memory vector index design tailored for multi-tenant queries that simultaneously achieves the two conflicting goals, low memory overhead and high performance for queries, vector insertion, and deletion. Curator indexes each tenant's vectors with a tenant-specific clustering tree and encodes these trees compactly as sub-trees of a shared clustering tree. Each tenant's clustering tree adapts dynamically to its unique vector distribution, while maintaining a low per-tenant memory footprint. Our evaluation, based on two widely used data sets, confirms that Curator delivers search performance on par with per-tenant indexing, while maintaining memory consumption at the same level as metadata filtering on a single, shared index.

EHRCon: Dataset for Checking Consistency between Unstructured Notes and Structured Tables in Electronic Health Records

Electronic Health Records (EHRs) are integral for storing comprehensive patient medical records, combining structured data (e.g., medications) with detailed clinical notes (e.g., physician notes). These elements are essential for straightforward data retrieval and provide deep, contextual insights into patient care. However, they often suffer from discrepancies due to unintuitive EHR system designs and human errors, posing serious risks to patient safety. To address this, we developed EHRCon, a new dataset and task specifically designed to ensure data consistency between structured tables and unstructured notes in EHRs. EHRCon was crafted in collaboration with healthcare professionals using the MIMIC-III EHR dataset, and includes manual annotations of 3,943 entities across 105 clinical notes checked against database entries for consistency. EHRCon has two versions, one using the original MIMIC-III schema, and another using the OMOP CDM schema, in order to increase its applicability and generalizability. Furthermore, leveraging the capabilities of large language models, we introduce CheckEHR, a novel framework for verifying the consistency between clinical notes and database tables. CheckEHR utilizes an eight-stage process and shows promising results in both few-shot and zero-shot settings. The code is available at https://github.com/dustn1259/EHRCon.

SCott: Accelerating Diffusion Models with Stochastic Consistency Distillation

The iterative sampling procedure employed by diffusion models (DMs) often leads to significant inference latency. To address this, we propose Stochastic Consistency Distillation (SCott) to enable accelerated text-to-image generation, where high-quality generations can be achieved with just 1-2 sampling steps, and further improvements can be obtained by adding additional steps. In contrast to vanilla consistency distillation (CD) which distills the ordinary differential equation solvers-based sampling process of a pretrained teacher model into a student, SCott explores the possibility and validates the efficacy of integrating stochastic differential equation (SDE) solvers into CD to fully unleash the potential of the teacher. SCott is augmented with elaborate strategies to control the noise strength and sampling process of the SDE solver. An adversarial loss is further incorporated to strengthen the sample quality with rare sampling steps. Empirically, on the MSCOCO-2017 5K dataset with a Stable Diffusion-V1.5 teacher, SCott achieves an FID (Frechet Inceptio Distance) of 22.1, surpassing that (23.4) of the 1-step InstaFlow (Liu et al., 2023) and matching that of 4-step UFOGen (Xue et al., 2023b). Moreover, SCott can yield more diverse samples than other consistency models for high-resolution image generation (Luo et al., 2023a), with up to 16% improvement in a qualified metric. The code and checkpoints are coming soon.

When the signal is in the noise: Exploiting Diffix's Sticky Noise

Anonymized data is highly valuable to both businesses and researchers. A large body of research has however shown the strong limits of the de-identification release-and-forget model, where data is anonymized and shared. This has led to the development of privacy-preserving query-based systems. Based on the idea of "sticky noise", Diffix has been recently proposed as a novel query-based mechanism satisfying alone the EU Article~29 Working Party's definition of anonymization. According to its authors, Diffix adds less noise to answers than solutions based on differential privacy while allowing for an unlimited number of queries. This paper presents a new class of noise-exploitation attacks, exploiting the noise added by the system to infer private information about individuals in the dataset. Our first differential attack uses samples extracted from Diffix in a likelihood ratio test to discriminate between two probability distributions. We show that using this attack against a synthetic best-case dataset allows us to infer private information with 89.4% accuracy using only 5 attributes. Our second cloning attack uses dummy conditions that conditionally strongly affect the output of the query depending on the value of the private attribute. Using this attack on four real-world datasets, we show that we can infer private attributes of at least 93% of the users in the dataset with accuracy between 93.3% and 97.1%, issuing a median of 304 queries per user. We show how to optimize this attack, targeting 55.4% of the users and achieving 91.7% accuracy, using a maximum of only 32 queries per user. Our attacks demonstrate that adding data-dependent noise, as done by Diffix, is not sufficient to prevent inference of private attributes. We furthermore argue that Diffix alone fails to satisfy Art. 29 WP's definition of anonymization. [...]

Blockchain-Based Federated Learning: Incentivizing Data Sharing and Penalizing Dishonest Behavior

With the increasing importance of data sharing for collaboration and innovation, it is becoming more important to ensure that data is managed and shared in a secure and trustworthy manner. Data governance is a common approach to managing data, but it faces many challenges such as data silos, data consistency, privacy, security, and access control. To address these challenges, this paper proposes a comprehensive framework that integrates data trust in federated learning with InterPlanetary File System, blockchain, and smart contracts to facilitate secure and mutually beneficial data sharing while providing incentives, access control mechanisms, and penalizing any dishonest behavior. The experimental results demonstrate that the proposed model is effective in improving the accuracy of federated learning models while ensuring the security and fairness of the data-sharing process. The research paper also presents a decentralized federated learning platform that successfully trained a CNN model on the MNIST dataset using blockchain technology. The platform enables multiple workers to train the model simultaneously while maintaining data privacy and security. The decentralized architecture and use of blockchain technology allow for efficient communication and coordination between workers. This platform has the potential to facilitate decentralized machine learning and support privacy-preserving collaboration in various domains.

A Framework for Fast and Stable Representations of Multiparameter Persistent Homology Decompositions

Topological data analysis (TDA) is an area of data science that focuses on using invariants from algebraic topology to provide multiscale shape descriptors for geometric data sets such as point clouds. One of the most important such descriptors is {\em persistent homology}, which encodes the change in shape as a filtration parameter changes; a typical parameter is the feature scale. For many data sets, it is useful to simultaneously vary multiple filtration parameters, for example feature scale and density. While the theoretical properties of single parameter persistent homology are well understood, less is known about the multiparameter case. In particular, a central question is the problem of representing multiparameter persistent homology by elements of a vector space for integration with standard machine learning algorithms. Existing approaches to this problem either ignore most of the multiparameter information to reduce to the one-parameter case or are heuristic and potentially unstable in the face of noise. In this article, we introduce a new general representation framework that leverages recent results on {\em decompositions} of multiparameter persistent homology. This framework is rich in information, fast to compute, and encompasses previous approaches. Moreover, we establish theoretical stability guarantees under this framework as well as efficient algorithms for practical computation, making this framework an applicable and versatile tool for analyzing geometric and point cloud data. We validate our stability results and algorithms with numerical experiments that demonstrate statistical convergence, prediction accuracy, and fast running times on several real data sets.

Enforcing public data archiving policies in academic publishing: A study of ecology journals

To improve the quality and efficiency of research, groups within the scientific community seek to exploit the value of data sharing. Funders, institutions, and specialist organizations are developing and implementing strategies to encourage or mandate data sharing within and across disciplines, with varying degrees of success. Academic journals in ecology and evolution have adopted several types of public data archiving policies requiring authors to make data underlying scholarly manuscripts freely available. Yet anecdotes from the community and studies evaluating data availability suggest that these policies have not obtained the desired effects, both in terms of quantity and quality of available datasets. We conducted a qualitative, interview-based study with journal editorial staff and other stakeholders in the academic publishing process to examine how journals enforce data archiving policies. We specifically sought to establish who editors and other stakeholders perceive as responsible for ensuring data completeness and quality in the peer review process. Our analysis revealed little consensus with regard to how data archiving policies should be enforced and who should hold authors accountable for dataset submissions. Themes in interviewee responses included hopefulness that reviewers would take the initiative to review datasets and trust in authors to ensure the completeness and quality of their datasets. We highlight problematic aspects of these thematic responses and offer potential starting points for improvement of the public data archiving process.

Equality before the Law: Legal Judgment Consistency Analysis for Fairness

In a legal system, judgment consistency is regarded as one of the most important manifestations of fairness. However, due to the complexity of factual elements that impact sentencing in real-world scenarios, few works have been done on quantitatively measuring judgment consistency towards real-world data. In this paper, we propose an evaluation metric for judgment inconsistency, Legal Inconsistency Coefficient (LInCo), which aims to evaluate inconsistency between data groups divided by specific features (e.g., gender, region, race). We propose to simulate judges from different groups with legal judgment prediction (LJP) models and measure the judicial inconsistency with the disagreement of the judgment results given by LJP models trained on different groups. Experimental results on the synthetic data verify the effectiveness of LInCo. We further employ LInCo to explore the inconsistency in real cases and come to the following observations: (1) Both regional and gender inconsistency exist in the legal system, but gender inconsistency is much less than regional inconsistency; (2) The level of regional inconsistency varies little across different time periods; (3) In general, judicial inconsistency is negatively correlated with the severity of the criminal charges. Besides, we use LInCo to evaluate the performance of several de-bias methods, such as adversarial learning, and find that these mechanisms can effectively help LJP models to avoid suffering from data bias.

Matching Table Metadata with Business Glossaries Using Large Language Models

Enterprises often own large collections of structured data in the form of large databases or an enterprise data lake. Such data collections come with limited metadata and strict access policies that could limit access to the data contents and, therefore, limit the application of classic retrieval and analysis solutions. As a result, there is a need for solutions that can effectively utilize the available metadata. In this paper, we study the problem of matching table metadata to a business glossary containing data labels and descriptions. The resulting matching enables the use of an available or curated business glossary for retrieval and analysis without or before requesting access to the data contents. One solution to this problem is to use manually-defined rules or similarity measures on column names and glossary descriptions (or their vector embeddings) to find the closest match. However, such approaches need to be tuned through manual labeling and cannot handle many business glossaries that contain a combination of simple as well as complex and long descriptions. In this work, we leverage the power of large language models (LLMs) to design generic matching methods that do not require manual tuning and can identify complex relations between column names and glossaries. We propose methods that utilize LLMs in two ways: a) by generating additional context for column names that can aid with matching b) by using LLMs to directly infer if there is a relation between column names and glossary descriptions. Our preliminary experimental results show the effectiveness of our proposed methods.

Detecting and Filtering Unsafe Training Data via Data Attribution

Large language models (LLMs) are vulnerable to unsafe training data that even small amounts of unsafe data can lead to harmful model behaviors. Detecting and filtering such unsafe training data is essential for trustworthy model development. Current state-of-the-art (SOTA) approaches typically rely on training moderation classifiers which requires significant computational overhead and are limited to predefined taxonomies, making them less adaptable to evolving safety concerns. Moreover, these classifiers lack insight into the training process, limiting their effectiveness in filtering unsafe data. To address these limitations, we propose DABUF, leveraging data attribution to detect and filter unsafe training data by attributing harmful model outputs to influential training data points. DABUF enables flexible identification of various unsafe data types without predefined taxonomies. However, in practice, model outputs can be complex with combined safe linguistic features and unsafe content, leading to reduced attribution accuracy. In such cases, DABUF will integrate moderation classifiers to identify a minimal subset of unsafe training data for targeted attribution (such as jailbreak). When model outputs are relatively straightforward, DABUF uses model outputs directly as the attribution targets. We evaluate the performance on two different tasks: in filtering jailbreaking training data and in identifying and mitigating gender bias. DABUF outperforms SOTA approaches by up to 7.5\% in detection AUPRC in jailbreaking scenarios, and 44.1\% in detecting gender bias. Moreover, retraining on DABUF-filtered data leads to higher model safety across experiments, underscoring its versatility in addressing a broad spectrum of unsafe data issues.

OpenDataLab: Empowering General Artificial Intelligence with Open Datasets

The advancement of artificial intelligence (AI) hinges on the quality and accessibility of data, yet the current fragmentation and variability of data sources hinder efficient data utilization. The dispersion of data sources and diversity of data formats often lead to inefficiencies in data retrieval and processing, significantly impeding the progress of AI research and applications. To address these challenges, this paper introduces OpenDataLab, a platform designed to bridge the gap between diverse data sources and the need for unified data processing. OpenDataLab integrates a wide range of open-source AI datasets and enhances data acquisition efficiency through intelligent querying and high-speed downloading services. The platform employs a next-generation AI Data Set Description Language (DSDL), which standardizes the representation of multimodal and multi-format data, improving interoperability and reusability. Additionally, OpenDataLab optimizes data processing through tools that complement DSDL. By integrating data with unified data descriptions and smart data toolchains, OpenDataLab can improve data preparation efficiency by 30\%. We anticipate that OpenDataLab will significantly boost artificial general intelligence (AGI) research and facilitate advancements in related AI fields. For more detailed information, please visit the platform's official website: https://opendatalab.com.